Ok, I believe I made some progress.
I found one more issue: PETSC_DIR was pointing toward an old macport
install of petsc
This is fixed now and here is what I have (without -E):
(petsc) barracuda:qgsolver aponte$ make
PYTHON=~/.miniconda3/envs/petsc/bin/python
PETSC_DIR=~/.miniconda3/envs/petsc build
env \
F77="" F77FLAGS="" \
F90="" F90FLAGS="" \
LDSHARED="" \
/Users/aponte/.miniconda3/envs/petsc/bin/python setup.py -q
build_ext --inplace
Reading .f2py_f2cmap ...
Mapping "integer(kind=HANDLE_KIND)" to "long"
Mapping "integer(kind=handle_kind)" to "long"
Successfully applied user defined changes from .f2py_f2cmap
In file included from
/Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from
/Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from
/Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from
build/src.macosx-10.9-x86_64-3.6/./fortranobject.h:13,
from ./timestepper_advmodule.c:18:
/Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: #warning "Using deprecated NumPy API, disable it by "
"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
In file included from
/Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from
/Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from
/Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from
build/src.macosx-10.9-x86_64-3.6/./fortranobject.h:13,
from build/src.macosx-10.9-x86_64-3.6/./fortranobject.c:2:
/Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: #warning "Using deprecated NumPy API, disable it by "
"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
build/src.macosx-10.9-x86_64-3.6/./fortranobject.c: In function
'format_def':
build/src.macosx-10.9-x86_64-3.6/./fortranobject.c:138:18: warning:
comparison between signed and unsigned integer expressions [-Wsign-compare]
if (size < sizeof(notalloc)) {
^
./timestepper_adv.F90:11.6:
use petsc
1
Fatal Error: Can't open module file 'petsc.mod' for reading at (1): No
such file or directory
./timestepper_adv.F90:11.6:
use petsc
1
Fatal Error: Can't open module file 'petsc.mod' for reading at (1): No
such file or directory
error: Command "/opt/local/bin/gfortran -Wall -g -fno-second-underscore
-DF2PY_REPORT_ON_ARRAY_COPY=1
-I/Users/aponte/.miniconda3/envs/petsc/include
-I/Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/petsc4py/include
-I. -Ibuild/src.macosx-10.9-x86_64-3.6/.
-I/Users/aponte/.miniconda3/envs/petsc/lib/python3.6/site-packages/numpy/core/include
-I/Users/aponte/.miniconda3/envs/petsc/include/python3.6m -c -c
./timestepper_adv.F90 -o
build/temp.macosx-10.9-x86_64-3.6/timestepper_adv.o
-Jbuild/temp.macosx-10.9-x86_64-3.6/
-Ibuild/temp.macosx-10.9-x86_64-3.6/" failed with exit status 1
--
Aurélien Ponte
Tel: (+33) 2 98 22 40 73
Fax: (+33) 2 98 22 44 96
UMR 6523, IFREMER
ZI de la Pointe du Diable
CS 10070
29280 Plouzané
